One afternoon in late July, Alex Gansa, the co-creator of the Showtime series Homeland, is in a bungalow on the 20th Century Fox lot in L.A., trying not to freak out. “Can I tell you something?” Gansa says between bites of his takeout lunch. “It’s the worst job, running a show. I don’t mean to sound self-pitying – but it’s been rough. I’m working on four or five episodes at once – just trying to keep the thing on the rails.” Gansa, a Princeton grad with the air of a kindly world-lit professor, has reason to be anxious. At the moment, the show’s cast and crew, including Emmy winners Claire Danes and Damian Lewis, are nearly 2,500 miles away in Charlotte, North Carolina, filming Episode Six of the show’s third season. Gansa and his writing staff are frantically scrambling to finish Episode Seven; Episode Eight, meanwhile, is a blank slate. “So if you sense a vague panic,” says Gansa, 52, “you would be correct.”

Since its premiere two years ago, Homeland has been acclaimed as one of the most risk-taking shows on TV. The series – which chronicles the tense back-and-forth between a brilliant, bipolar CIA agent and a rescued Marine POW who’s a sleeper agent for Al Qaeda – encompasses every hot-button post-9/11 political issue: domestic terrorism; the efficacy of torture; wiretaps and the civil-liberties debate; PTSD; and the legality and morality of lethal drone strikes. President Obama is a fan of the show. Last season, viewership increased every episode, and it was nominated for 11 Emmys, including nods for best dramatic series, best writing and directing, and best acting by all four of its leads.

And yet there’s also a creeping sense that Homeland has gone slightly off the rails. Far-fetched storytelling devices (BlackBerry video chats, an assassination-by-pacemaker) and larger-than-life subplots (a massive gun battle at a small-town tailor, a teenage SUV manslaughter) have left many fans grumbling about plausibility. And the constantly escalating love affair between Danes’ CIA analyst, Carrie Mathison, and Lewis’ would-be terrorist, Sgt. Nicholas Brody, whom she’s supposed to be chasing, is nearing melodramatic levels. “I know a lot of people have talked about how absurd it was that Brody and Carrie were considering the possibility of living happily ever after,” Gansa says. “Well, that was the intention! These two people are trying to dupe themselves in front of your eyes. So for viewers who were watching that going, ‘Are they fucking crazy?’ –the answer to that is ‘yes!'”

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Gansa admits that some of the criticism of the second story arc might be justified. “The first season we had the luxury of time, and a much clearer idea of what it would be,” he says. “The third season we’re inventing day to day, and it’s terrifying.”

In fact, he says, some of the plot holes that worry him most are ones nobody brings up. “The fact that you had two Marines turned to Al Qaeda in captivity – that just struck me as bullshit. I didn’t believe it even as we were writing it.” He also had a problem with the commando raid on the tailor’s, which was too 24 for his taste. (He and Homeland co-creator Howard Gordon are both veterans of that show.) “But the pacemaker thing,” Gansa says, “we tend to be very hard on ourselves here, and that didn’t even cause a ripple.”

For its third season, Homeland faces more challenges than ever – perhaps the biggest of which is the loss of key writers. Meredith Stiehm left to run her own show, The Bridge, on FX. Executive producer Michael Cuesta is directing a feature film. Writer Henry Bromell, the son of a former CIA station chief in the Middle East who brought verisimilitude to the show, died in March of a heart attack. “We miss him every day,” Gansa says.

Mostly, though, Homeland will need to find a way to succeed without the chemistry between its two stars. As Season Three opens, Brody – whom Gansa has tried to kill off twice – is in hiding, while Carrie is investigating the worst terror attack since 9/11. Gansa says that, six weeks in, Danes and Lewis haven’t even been on set together.

“I don’t know how much of that love story – and I use ‘love’ in quotation marks – there is left to tell,” he says. Instead, they’re shifting focus back to the true franchise of the show: Carrie and her boss, Saul Berenson (Mandy Patinkin), out chasing bad guys. This year, Gansa says, that will be Iran: The attack on the CIA last season will be revealed to be state-sponsored, and Saul and Carrie are tasked with figuring out how to respond.

For Gansa, the drastic change is part of the fun. “I don’t believe there’s an appetite to do the same story again,” he says. “So the show is gonna have to reinvent itself on some level.”